epub or pdf?

Here's my goal. I have a magazine created in InDesign (CS3) and I'd like to
create an e-zine/e-pub from it. I like the ease of Acrobat, along with the
security that can be added, and I like how the reader sees the document in
Digital Editions (it looks more like a magazine).
When I use Cross-media Export (XHTML/Digital Editions) in InDesign, all my
photos and layouts and everything are eliminated when I view it in Editions. I
understand that I need to have styles created for each instance, but it's not
even translating the styles that I do have. The same thing happens when I
Cross-media Export using XHTML/Dreamweaver.

For the limitations of InDesign, I recommend you post in the InDesign
forum.